changing command name classify.shared to classifyrf.shared

[mothur.git] / otuassociationcommand.h

diff --git a/otuassociationcommand.h b/otuassociationcommand.h
index 7aaa88a61c37a21ec6a9af5d1bb8f0c90066c222..e9cdb2a290fb5a778bf936e3040b97433121be32 100644 (file)
--- a/otuassociationcommand.h
+++ b/otuassociationcommand.h
@@ -25,7 +25,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "otu.association";                     }
        string getCommandCategory()             { return "Hypothesis Testing";          }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Otu.association"; }
        string getDescription()         { return "calculate the correlation coefficient for the otus in a shared/relabund file"; }
        
@@ -33,15 +35,20 @@ public:
        void help() { m->mothurOut(getHelpString()); }  
 private:
        
-       string sharedfile, relabundfile, groups, label, inputFileName, outputDir, method;
+       string sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method;
        bool abort, pickedGroups, allLines;
+    double cutoff;
        set<string> labels;
+    vector<SharedRAbundFloatVector*> metadataLookup;
+    vector< vector< double> > metadata;
        
-       vector<string> outputNames, Groups;
+       vector<string> outputNames, Groups, metadataLabels;
        int processShared();
        int process(vector<SharedRAbundVector*>&);
        int processRelabund();
        int process(vector<SharedRAbundFloatVector*>&);
+    int readMetadata();
+    int getMetadata();
        
 };